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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs11541565

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:14092870 (GRCh38.p14) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.063516 (16812/264690, TOPMED)
G=0.058420 (7844/134268, GnomAD)
G=0.02471 (1255/50786, GnomAD_exome) (+ 13 more)
G=0.01993 (560/28098, 14KJPN)
G=0.03279 (659/20100, ALFA)
G=0.02137 (358/16754, 8.3KJPN)
G=0.0703 (450/6404, 1000G_30x)
G=0.0667 (334/5008, 1000G)
G=0.0011 (5/4480, Estonian)
G=0.0261 (75/2876, KOREAN)
G=0.0312 (57/1828, Korea1K)
G=0.0563 (83/1474, ExAC)
G=0.007 (4/600, NorthernSweden)
G=0.002 (1/534, MGP)
G=0.023 (5/216, Qatari)
A=0.45 (18/40, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PRKACA : 3 Prime UTR Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 20100 A=0.96721 G=0.03279
European Sub 15228 A=0.99803 G=0.00197
African Sub 2972 A=0.8062 G=0.1938
African Others Sub 116 A=0.767 G=0.233
African American Sub 2856 A=0.8078 G=0.1922
Asian Sub 136 A=0.985 G=0.015
East Asian Sub 98 A=0.98 G=0.02
Other Asian Sub 38 A=1.00 G=0.00
Latin American 1 Sub 146 A=0.952 G=0.048
Latin American 2 Sub 610 A=0.993 G=0.007
South Asian Sub 98 A=0.98 G=0.02
Other Sub 910 A=0.958 G=0.042


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 A=0.936484 G=0.063516
gnomAD - Genomes Global Study-wide 134268 A=0.941580 G=0.058420
gnomAD - Genomes European Sub 73490 A=0.99856 G=0.00144
gnomAD - Genomes African Sub 39502 A=0.81307 G=0.18693
gnomAD - Genomes American Sub 12878 A=0.98261 G=0.01739
gnomAD - Genomes Ashkenazi Jewish Sub 3268 A=0.9960 G=0.0040
gnomAD - Genomes East Asian Sub 3094 A=0.9842 G=0.0158
gnomAD - Genomes Other Sub 2036 A=0.9666 G=0.0334
gnomAD - Exomes Global Study-wide 50786 A=0.97529 G=0.02471
gnomAD - Exomes European Sub 24520 A=0.99837 G=0.00163
gnomAD - Exomes Asian Sub 11222 A=0.98236 G=0.01764
gnomAD - Exomes American Sub 7060 A=0.9898 G=0.0102
gnomAD - Exomes African Sub 4918 A=0.8115 G=0.1885
gnomAD - Exomes Other Sub 1614 A=0.9913 G=0.0087
gnomAD - Exomes Ashkenazi Jewish Sub 1452 A=0.9972 G=0.0028
14KJPN JAPANESE Study-wide 28098 A=0.98007 G=0.01993
Allele Frequency Aggregator Total Global 20100 A=0.96721 G=0.03279
Allele Frequency Aggregator European Sub 15228 A=0.99803 G=0.00197
Allele Frequency Aggregator African Sub 2972 A=0.8062 G=0.1938
Allele Frequency Aggregator Other Sub 910 A=0.958 G=0.042
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.993 G=0.007
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.952 G=0.048
Allele Frequency Aggregator Asian Sub 136 A=0.985 G=0.015
Allele Frequency Aggregator South Asian Sub 98 A=0.98 G=0.02
8.3KJPN JAPANESE Study-wide 16754 A=0.97863 G=0.02137
1000Genomes_30x Global Study-wide 6404 A=0.9297 G=0.0703
1000Genomes_30x African Sub 1786 A=0.7928 G=0.2072
1000Genomes_30x Europe Sub 1266 A=0.9992 G=0.0008
1000Genomes_30x South Asian Sub 1202 A=0.9759 G=0.0241
1000Genomes_30x East Asian Sub 1170 A=0.9829 G=0.0171
1000Genomes_30x American Sub 980 A=0.969 G=0.031
1000Genomes Global Study-wide 5008 A=0.9333 G=0.0667
1000Genomes African Sub 1322 A=0.7950 G=0.2050
1000Genomes East Asian Sub 1008 A=0.9802 G=0.0198
1000Genomes Europe Sub 1006 A=0.9980 G=0.0020
1000Genomes South Asian Sub 978 A=0.978 G=0.022
1000Genomes American Sub 694 A=0.973 G=0.027
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9989 G=0.0011
KOREAN population from KRGDB KOREAN Study-wide 2876 A=0.9739 G=0.0261
Korean Genome Project KOREAN Study-wide 1828 A=0.9688 G=0.0312
ExAC Global Study-wide 1474 A=0.9437 G=0.0563
ExAC Europe Sub 850 A=0.998 G=0.002
ExAC African Sub 370 A=0.786 G=0.214
ExAC Asian Sub 170 A=0.988 G=0.012
ExAC American Sub 70 A=1.00 G=0.00
ExAC Other Sub 14 A=1.00 G=0.00
Northern Sweden ACPOP Study-wide 600 A=0.993 G=0.007
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.998 G=0.002
Qatari Global Study-wide 216 A=0.977 G=0.023
SGDP_PRJ Global Study-wide 40 A=0.45 G=0.55
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 19 NC_000019.10:g.14092870A>G
GRCh37.p13 chr 19 NC_000019.9:g.14203682A>G
PRKACA RefSeqGene NG_029699.1:g.29878T>C
GRCh38.p14 chr 19 fix patch HG109_PATCH NW_021160022.1:g.305029A>G
Gene: PRKACA, protein kinase cAMP-activated catalytic subunit alpha (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PRKACA transcript variant 1 NM_002730.4:c.*242= N/A 3 Prime UTR Variant
PRKACA transcript variant 2 NM_207518.3:c.*242= N/A 3 Prime UTR Variant
PRKACA transcript variant 3 NM_001304349.2:c.*242= N/A 3 Prime UTR Variant
PRKACA transcript variant X1 XM_017026948.2:c.*242= N/A 3 Prime UTR Variant
PRKACA transcript variant X2 XM_047439070.1:c.*242= N/A 3 Prime UTR Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement A= G
GRCh38.p14 chr 19 NC_000019.10:g.14092870= NC_000019.10:g.14092870A>G
GRCh37.p13 chr 19 NC_000019.9:g.14203682= NC_000019.9:g.14203682A>G
PRKACA RefSeqGene NG_029699.1:g.29878= NG_029699.1:g.29878T>C
PRKACA transcript variant 1 NM_002730.4:c.*242= NM_002730.4:c.*242T>C
PRKACA transcript variant 1 NM_002730.3:c.*242= NM_002730.3:c.*242T>C
PRKACA transcript variant 2 NM_207518.3:c.*242= NM_207518.3:c.*242T>C
PRKACA transcript variant 2 NM_207518.2:c.*242= NM_207518.2:c.*242T>C
PRKACA transcript variant 2 NM_207518.1:c.*242= NM_207518.1:c.*242T>C
PRKACA transcript variant 3 NM_001304349.2:c.*242= NM_001304349.2:c.*242T>C
PRKACA transcript variant 3 NM_001304349.1:c.*242= NM_001304349.1:c.*242T>C
GRCh38.p14 chr 19 fix patch HG109_PATCH NW_021160022.1:g.305029= NW_021160022.1:g.305029A>G
PRKACA transcript variant X1 XM_017026948.2:c.*242= XM_017026948.2:c.*242T>C
PRKACA transcript variant X1 XM_017026948.1:c.*242= XM_017026948.1:c.*242T>C
PRKACA transcript variant X2 XM_047439070.1:c.*242= XM_047439070.1:c.*242T>C
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

41 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 PGA-UW-FHCRC ss60197911 Oct 18, 2006 (130)
2 GMI ss155636317 Dec 01, 2009 (131)
3 COMPLETE_GENOMICS ss169139252 Jul 04, 2010 (132)
4 1000GENOMES ss228051657 Jul 14, 2010 (132)
5 1000GENOMES ss243830299 Jul 15, 2010 (132)
6 GMI ss283132778 May 04, 2012 (137)
7 TISHKOFF ss565869618 Apr 25, 2013 (138)
8 SSMP ss661725553 Apr 25, 2013 (138)
9 JMKIDD_LAB ss1081775071 Aug 21, 2014 (142)
10 1000GENOMES ss1362459024 Aug 21, 2014 (142)
11 EVA_EXAC ss1693419929 Apr 01, 2015 (144)
12 EVA_DECODE ss1698173954 Apr 01, 2015 (144)
13 EVA_MGP ss1711501222 Apr 01, 2015 (144)
14 HAMMER_LAB ss1809220557 Sep 08, 2015 (146)
15 WEILL_CORNELL_DGM ss1937599391 Feb 12, 2016 (147)
16 JJLAB ss2029571305 Sep 14, 2016 (149)
17 GNOMAD ss2743710631 Nov 08, 2017 (151)
18 GNOMAD ss2750096558 Nov 08, 2017 (151)
19 GNOMAD ss2960782829 Nov 08, 2017 (151)
20 AFFY ss2985767138 Nov 08, 2017 (151)
21 SWEGEN ss3017147182 Nov 08, 2017 (151)
22 EGCUT_WGS ss3683973551 Jul 13, 2019 (153)
23 ACPOP ss3742878132 Jul 13, 2019 (153)
24 EVA ss3755842853 Jul 13, 2019 (153)
25 KHV_HUMAN_GENOMES ss3821097873 Jul 13, 2019 (153)
26 SGDP_PRJ ss3887825182 Apr 27, 2020 (154)
27 KRGDB ss3937811622 Apr 27, 2020 (154)
28 KOGIC ss3980906229 Apr 27, 2020 (154)
29 EVA ss3986079538 Apr 26, 2021 (155)
30 TOPMED ss5068886189 Apr 26, 2021 (155)
31 TOMMO_GENOMICS ss5226884060 Apr 26, 2021 (155)
32 1000G_HIGH_COVERAGE ss5306598268 Oct 16, 2022 (156)
33 EVA ss5433738295 Oct 16, 2022 (156)
34 HUGCELL_USP ss5499212529 Oct 16, 2022 (156)
35 1000G_HIGH_COVERAGE ss5612037438 Oct 16, 2022 (156)
36 SANFORD_IMAGENETICS ss5662031899 Oct 16, 2022 (156)
37 TOMMO_GENOMICS ss5785214201 Oct 16, 2022 (156)
38 YY_MCH ss5817431734 Oct 16, 2022 (156)
39 EVA ss5840293863 Oct 16, 2022 (156)
40 EVA ss5927404873 Oct 16, 2022 (156)
41 EVA ss5953451578 Oct 16, 2022 (156)
42 1000Genomes NC_000019.9 - 14203682 Oct 12, 2018 (152)
43 1000Genomes_30x NC_000019.10 - 14092870 Oct 16, 2022 (156)
44 Genetic variation in the Estonian population NC_000019.9 - 14203682 Oct 12, 2018 (152)
45 ExAC NC_000019.9 - 14203682 Oct 12, 2018 (152)
46 gnomAD - Genomes NC_000019.10 - 14092870 Apr 26, 2021 (155)
47 gnomAD - Exomes NC_000019.9 - 14203682 Jul 13, 2019 (153)
48 KOREAN population from KRGDB NC_000019.9 - 14203682 Apr 27, 2020 (154)
49 Korean Genome Project NC_000019.10 - 14092870 Apr 27, 2020 (154)
50 Medical Genome Project healthy controls from Spanish population NC_000019.9 - 14203682 Apr 27, 2020 (154)
51 Northern Sweden NC_000019.9 - 14203682 Jul 13, 2019 (153)
52 Qatari NC_000019.9 - 14203682 Apr 27, 2020 (154)
53 SGDP_PRJ NC_000019.9 - 14203682 Apr 27, 2020 (154)
54 8.3KJPN NC_000019.9 - 14203682 Apr 26, 2021 (155)
55 14KJPN NC_000019.10 - 14092870 Oct 16, 2022 (156)
56 TopMed NC_000019.10 - 14092870 Apr 26, 2021 (155)
57 ALFA NC_000019.10 - 14092870 Apr 26, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID History Updated (Build)
rs41296318 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss169139252, ss283132778, ss1698173954 NC_000019.8:14064681:A:G NC_000019.10:14092869:A:G (self)
75840677, 29711799, 3911347, 13025006, 44989016, 616982, 16162997, 19641313, 39842162, 84853367, ss228051657, ss243830299, ss565869618, ss661725553, ss1081775071, ss1362459024, ss1693419929, ss1711501222, ss1809220557, ss1937599391, ss2029571305, ss2743710631, ss2750096558, ss2960782829, ss2985767138, ss3017147182, ss3683973551, ss3742878132, ss3755842853, ss3887825182, ss3937811622, ss3986079538, ss5226884060, ss5433738295, ss5662031899, ss5840293863, ss5953451578 NC_000019.9:14203681:A:G NC_000019.10:14092869:A:G (self)
99563373, 534882865, 37284230, 119051305, 284431853, 1660854091, ss3821097873, ss3980906229, ss5068886189, ss5306598268, ss5499212529, ss5612037438, ss5785214201, ss5817431734, ss5927404873 NC_000019.10:14092869:A:G NC_000019.10:14092869:A:G (self)
ss60197911, ss155636317 NT_011295.11:5466483:A:G NC_000019.10:14092869:A:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs11541565

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top▲ Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post761+d5e8e07